Difference between OpenEXR and OpenEXR Multilayer file format?
It was noted in the comments but in short, use Multilayer when you want to bundle multiple render passes in one file. It's worth noting that some programs can read EXR files, but not Multilayer EXR files. For this reason, I use  OpenEXR for non-lossy high color depth renders, and pretty much don't use OpenEXR Multilayer. The main purpose of Multilayer is to keep all the corresponding passes together for each frame, which is useful for working with other compositing software that then extracs and uses each pass.